hiraksarkar

#API created by @apfejes (Anthony Fejes) on top of my half-cooked script
#python ebi_url_from_srr.py --file srr_list.txt | xargs -I {} wget {}

import argparse
def prepareURL(srr_name, prefix="ftp://ftp.sra.ebi.ac.uk/vol1/fastq/"):
    dir_1=srr_name[:6]
    dir_2=""
    url=""
    num_digits=sum(s.isdigit() for s in srr_name)
    if(num_digits == 6):

hiraksarkar

DROP TABLE IF EXISTS emp;

CREATE TABLE emp (
  empno decimal(4,0) NOT NULL,
  ename varchar(10) default NULL,
  job varchar(9) default NULL,
  mgr decimal(4,0) default NULL,
  hiredate date default NULL,
  sal decimal(7,2) default NULL,
  comm decimal(7,2) default NULL,

hiraksarkar

Note

I have changed only two directory names from the original post to be found here

Open account with ngrok.com

Get the autorization code after creating a free account with ngork. You will meet with a screen like following

Install stuff (in colab)

hiraksarkar

plt.figure(figsize=(8, 8))
df = np.log(variance_trio_df[['var_mean','merged_var']]+1)
df.loc[:,'color'] = 'b'
df.loc[(df.merged_var - df.var_mean) < -1, 'color'] = 'r'
colors = ["b", "r"]
customPalette = sns.set_palette(sns.color_palette(colors))
ax = sns.scatterplot(
    x = 'var_mean', 
    y = 'merged_var',
    data = df,

hiraksarkar

#!/usr/bin/bash

tfile=$1
usr=`rg "(\d+\.\d+)user" $tfile -or '$1'`
sys=`rg "(\d+\.\d+)system" $tfile -or '$1'`
elap=`rg "([\d:\.]+)elapsed" $tfile -or '$1'`
mem=`rg "(\d+)maxresident" $tfile -or '$1'`

tot_elap=`echo "$elap" | sed -E 's/(.*):(.+):(.+)/\1*3600+\2*60+\3/;s/(.+):(.+)/\1*60+\2/' | bc`

hiraksarkar

Keybase proof

I hereby claim:

• I am hiraksarkar on github.
• I am hiraksarkar (https://keybase.io/hiraksarkar) on keybase.
• I have a public key whose fingerprint is 4152 B3E7 7BE1 83B0 1E53 8B80 2EDB 3721 028D 527A

To claim this, I am signing this object:

hiraksarkar

use ndarray::prelude::*;

fn std1d(a: ArrayView1<'_, f64>) -> f64 {
    let n = a.len() as f64;
    if n == 0. {
        return 0.;
    }
    let mean = a.sum() / n;
    (a.fold(0., |acc, &x| acc + (x - mean).powi(2)) / n).sqrt()
}

hiraksarkar

import glob
import pandas as pd
import tqdm
#from pyfasta import Fasta
#%matplotlib inline
import matplotlib
matplotlib.use('agg')
import matplotlib.pyplot as plt
import seaborn as sns
from collections import defaultdict

hiraksarkar

SPC s c remove highlight

**** Files manipulations key bindings
Files manipulation commands (start with ~f~):

| Key Binding | Description                                                    |
|-------------+----------------------------------------------------------------|
| ~SPC f c~   | copy current file to a different location                      |
| ~SPC f C d~ | convert file from unix to dos encoding                         |
| ~SPC f C u~ | convert file from dos to unix encoding                         |

hiraksarkar

PATH that worked in newton

export PATH="/home/linuxbrew/.linuxbrew/bin/:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/usr/lib/jvm/java-8-oracle/bin:/usr/lib/jvm/java-8-oracle/db/bin:/usr/lib/jvm/java-8-oracle/jre/bin:/home/linuxbrew/.linuxbrew/bin/:/home/linuxbrew/.linuxbrew/bin/"

hello

Transferring files from newton

shuf -n 1000 /bio2/home/mferdman/paired.bulk-only > oct_28/file_list\